Movatterモバイル変換

################################################################################################################################################################## Running command:######   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:treekoR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings treekoR_1.18.0.tar.gz###############################################################################################################################################################* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/treekoR.Rcheck’* using R version 4.5.2 Patched (2025-11-04 r88984)* using platform: aarch64-apple-darwin20* R was compiled by    Apple clang version 16.0.0 (clang-1600.0.26.6)    GNU Fortran (GCC) 14.2.0* running under: macOS Ventura 13.7.8* using session charset: UTF-8* using option ‘--no-vignettes’* checking for file ‘treekoR/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘treekoR’ version ‘1.18.0’* package encoding: UTF-8* checking package namespace information ... OK* checking package dependencies ... OK* checking if this is a source package ... OK* checking if there is a namespace ... OK* checking for hidden files and directories ... OK* checking for portable file names ... OK* checking for sufficient/correct file permissions ... OK* checking whether package ‘treekoR’ can be installed ... OK* checking installed package size ... OK* checking package directory ... OK* checking ‘build’ directory ... OK* checking DESCRIPTION meta-information ... OK* checking top-level files ... OK* checking for left-over files ... OK* checking index information ... OK* checking package subdirectories ... OK* checking code files for non-ASCII characters ... OK* checking R files for syntax errors ... OK* checking whether the package can be loaded ... OK* checking whether the package can be loaded with stated dependencies ... OK* checking whether the package can be unloaded cleanly ... OK* checking whether the namespace can be loaded with stated dependencies ... OK* checking whether the namespace can be unloaded cleanly ... OK* checking dependencies in R code ... OK* checking S3 generic/method consistency ... OK* checking replacement functions ... OK* checking foreign function calls ... OK* checking R code for possible problems ... NOTEaddFreqBars: no visible binding for global variable ‘freq’addFreqBars: no visible binding for global variable ‘xmax’addFreqBars: no visible binding for global variable ‘y’addFreqBars: no visible binding for global variable ‘xmin’addFreqBars: no visible binding for global variable ‘ymin’addFreqBars: no visible binding for global variable ‘ymax’addFreqBars: no visible binding for global variable ‘x_label’addFreqBars: no visible binding for global variable ‘freq_label’addHeatMap: no visible binding for global variable ‘variable’addHeatMap: no visible binding for global variable ‘value’addHeatMap: no visible binding for global variable ‘y’addHeatMap: no visible binding for global variable ‘label’addHeatMap: no visible binding for global variable ‘.’addHeatMap: no visible binding for global variable ‘x’colourTree: no visible binding for global variable ‘stat_parent’colourTree: no visible binding for global variable ‘x’colourTree: no visible binding for global variable ‘y’colourTree: no visible binding for global variable ‘stat_total’colourTree: no visible binding for global variable ‘label’getCellGMeans: no visible binding for global variable ‘cluster_id’getCellGMeans: no visible binding for global variable ‘sample_id’getCellProp: no visible binding for global variable ‘cluster_id’getCellProp: no visible binding for global variable ‘sample_id’getCellProp: no visible binding for global variable ‘.’getClusterTree: no visible binding for global variable ‘cluster_id’plotInteractiveHeatmap: no visible binding for global variable ‘label’plotInteractiveHeatmap: no visible binding for global variable ‘node’plotSigScatter: no visible binding for global variable ‘stat_total’plotSigScatter: no visible binding for global variable ‘stat_parent’plotSigScatter: no visible binding for global variable ‘isTip’plotSigScatter: no visible binding for global variable ‘label’runEdgeRTests: no visible binding for global variable ‘PValue’runEdgeRTests: no visible binding for global variable ‘logFC’runEdgeRTests: no visible binding for global variable ‘node’runEdgeRTests: no visible binding for global variable ‘stat_parent’runEdgeRTests: no visible binding for global variable ‘pval_parent’runEdgeRTests: no visible binding for global variable ‘FDR_parent’runEdgeRTests: no visible binding for global variable ‘PValue_total’runEdgeRTests: no visible binding for global variable ‘logFC_total’runEdgeRTests: no visible binding for global variable ‘stat_total’runEdgeRTests: no visible binding for global variable ‘pval_total’runEdgeRTests: no visible binding for global variable ‘FDR_total’runGLMMTests: no visible binding for global variable ‘isTip’runGLMMTests: no visible binding for global variable ‘node’Undefined global functions or variables:  . FDR_parent FDR_total PValue PValue_total cluster_id freq freq_label  isTip label logFC logFC_total node pval_parent pval_total sample_id  stat_parent stat_total value variable x x_label xmax xmin y ymax ymin* checking Rd files ... OK* checking Rd metadata ... OK* checking Rd cross-references ... OK* checking for missing documentation entries ... OK* checking for code/documentation mismatches ... OK* checking Rd \usage sections ... OK* checking Rd contents ... OK* checking for unstated dependencies in examples ... OK* checking contents of ‘data’ directory ... OK* checking data for non-ASCII characters ... OK* checking data for ASCII and uncompressed saves ... OK* checking files in ‘vignettes’ ... OK* checking examples ... OKExamples with CPU (user + system) or elapsed time > 5s                        user system elapsedplotInteractiveHeatmap 4.881  0.291   7.721colourTree             4.393  0.108   6.272getCellGMeans          4.294  0.075   6.437* checking for unstated dependencies in ‘tests’ ... OK* checking tests ...  Running ‘testthat.R’ OK* checking for unstated dependencies in vignettes ... OK* checking package vignettes ... OK* checking running R code from vignettes ... SKIPPED* checking re-building of vignette outputs ... SKIPPED* checking PDF version of manual ... OK* DONEStatus: 1 NOTESee  ‘/Users/biocbuild/bbs-3.22-bioc/meat/treekoR.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL treekoR###############################################################################################################################################################* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’* installing *source* package ‘treekoR’ ...** this is package ‘treekoR’ version ‘1.18.0’** using staged installation** R** data** inst** byte-compile and prepare package for lazy loading** help*** installing help indices** building package indices** installing vignettes** testing if installed package can be loaded from temporary location** testing if installed package can be loaded from final location** testing if installed package keeps a record of temporary installation path* DONE (treekoR)

R version 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"Copyright (C) 2025 The R Foundation for Statistical ComputingPlatform: aarch64-apple-darwin20R is free software and comes with ABSOLUTELY NO WARRANTY.You are welcome to redistribute it under certain conditions.Type 'license()' or 'licence()' for distribution details.R is a collaborative project with many contributors.Type 'contributors()' for more information and'citation()' on how to cite R or R packages in publications.Type 'demo()' for some demos, 'help()' for on-line help, or'help.start()' for an HTML browser interface to help.Type 'q()' to quit R.> library(testthat)> library(treekoR)> > test_check("treekoR")[ FAIL 0 | WARN 0 | SKIP 0 | PASS 40 ]> > proc.time()   user  system elapsed  28.279   1.244  40.589